caa05e37c4fe0649d3b26e69712244d90291b1b5
jnavarr5
  Tue Sep 1 14:52:44 2026 -0700
Fixing broken links that I found, no Redmine

diff --git docs/tutorials/customTrackTutorial.md docs/tutorials/customTrackTutorial.md
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 % UCSC Genome Browser Custom Track Tutorial
 
 The UCSC Genome Browser allows users to load their own annotations by adding
-[Custom Tracks](../cgi-bin/hgCustom). Custom tracks work well for quickly displaying data and are
+[Custom Tracks](/cgi-bin/hgCustom). Custom tracks work well for quickly displaying data and are
 automatically discarded 48 hours after the last time they were accessed.
  
 This tutorial introduces the Custom Track interface and demonstrates how to:
 
 - Select a genome and assembly
 - Define a region of interest
 - Format the custom track
 - Load a custom track into the Genome Browser
 - Manage custom tracks
 
 ## Learning materials
 
 <div class="row" style="padding-top: 15px">
 <div class="col-md-4">
 <div class="panel panel-default" style="padding-bottom: 10px">
 <h3 class="panel-title" style="width: 100%;">Custom Track Overview</h3>
 
 A screenshot highlighting the layout and key elements of the Custom Track interface.
 
 <p style="text-align: end">
 <button>[View](#custom-track-overview)</button>
 </p>
 </div>
 </div>
 
 <div class="col-md-4">
 <div class="panel panel-default" style="padding-bottom: 10px">
 <h3 class="panel-title" style="width: -webkit-fill-available;">Guided Walkthrough</h3>
 
 Step-by-step guidance for using the Custom Track interface to upload data for your analysis.
 
 <p style="text-align: end">
 <button>[View](#guided-walkthrough)</button>
 </p>
 </div>
 </div>
 
 <div class="col-md-4">
 <div class="panel panel-default" style="padding-bottom: 10px">
 <h3 class="panel-title" style="width: -webkit-fill-available;">Interactive Tutorial</h3>
 
 An in-browser walkthrough that introduces the Custom Track interface and workflow.
 
 <p style="text-align: end">
 <button>[View](/cgi-bin/hgCustom?db=hg19&startCustomTutorial=true&hgct_do_add=1)</button>
 </p>
 </div>
 </div>
 </div>
 
 ## Custom Track Overview
 
 <h6>Add Custom Tracks</h6>
 ``` image
 src=/images/tutorialImages/hgCustomAnnotated_pt1.png
 width=65%
 ```
 <h6>Manage Custom Tracks</h6>
 ``` image
 src=/images/tutorialImages/hgCustomAnnotated_pt2.png
 width=65%
 ```
 
 ---
 
 ## Guided Walkthrough
 
 
 <div class="row">
   <div class="col-md-6">
 ### Step 1: Select Your Assembly
   Use the **Change selected genome** search box to switch assemblies. Type a species name, common
   name, or assembly ID, then choose one from the list. **Current Genome** shows which assembly is
   active.
 
   </div>
 
   <div class="col-md-6">
   ```image
   src=/images/tutorialImages/gif/hgCustomStep1.gif
   width=90%
   ```
 </div>
 </div>
 
 ---
 
 
 <div class="row">
   <div class="col-md-6">
   ```image
   src=/images/tutorialImages/gif/hgCustomStep2.gif
   width=90%
   ```
   </div>
 
   <div class="col-md-6">
 ### Step 2: Create a browser line
   The [browser line](/goldenPath/help/customTrack.html#BROWSER) controls where you are first taken
   after uploading the custom track. This step controls the aspects of the overall display window.
     
   For example, if the browser line `browser position chr22:1-20000` is used, 
   the Genome Browser window will initially display the first 20,000 bases of chromosome 22.
 
   Browser lines are in the format:
 
     browser attribute_name attribute_value(s)
   </div>
 </div>
 
 ---
 
 ### The track line
 
 Along with the browser line, a **track line** sits above your data and sets what the track is
 called and how it looks. It is optional for a quick look, but worth adding if you plan to keep
 or share the track. Common attributes:
 
 - `name` — the short label shown to the left of the track
 - `description` — the longer text shown in the track's title and details page
 - `visibility` — how the track is drawn: `hide`, `dense`, `squish`, `pack`, or `full`
 - `color` — the feature color as RGB values, for example `color=0,0,255` for blue
 
 A track line looks like:
 
     track name="My variants" description="Sample calls" visibility=pack color=0,0,255
 
 For bigBed, bigWig, bigGenePred, CRAM, BAM, and VCF files you can skip the track line and
 paste just the URL to the file, one per line.
 
 ---
 
 
 <div class="row">
   <div class="col-md-6">
 ### Step 3: Format the Data
 
   The annotation data must be formatted into one of the [supporting formats](/FAQ/FAQformat.html).
   For many formats, chromosome names can either be UCSC-style names (e.g. 'chr1', 'chrX') or
   [aliases](/FAQ/FAQcustom.html#custom12) from other sources (e.g. '1' or 'NC\_000001.11').
   
   While most data types can be uploaded directly to UCSC, any of the binary-indexed files
   must be hosted on an external server. This includes formats such as bigBed, bigWig, BAM, VCF,
   and other big\* files. 
 
   A few hosting resources that we recommend can be found on the
   [Hosting](/goldenPath/help/hgTrackHubHelp.html#Hosting) help page.
 
   </div>
 
   <div class="col-md-6">
   ```image
   src=/images/tutorialImages/gif/hgCustomStep3.gif
   width=90%
   ```
   </div>
 </div>
 
 ---
 
 
 <div class="row">
   <div class="col-md-6">
   ```image
   src=/images/tutorialImages/gif/hgCustomStep4.gif
   width=90%
   ```
   </div>
 
   <div class="col-md-6">
 ### Step 4: Load the custom track
   Once the Browser and track lines are created, you can upload the custom track to the UCSC 
   Genome Browser using the dialogue box or the <button>Choose File</button> button to upload the
   custom track file. 
 
   When using a custom track file, you can also paste the URL to the custom track to quickly load
   your annotations. 
 
   We recommend adding documentation to your custom annotation tracks, especially if you intend
   to share the annotations with other collaborators. 
 
   </div>
 </div>
 
 ---
 
 <div class="row">
   <div class="col-md-6">
 ### Step 5: Manage custom tracks page
   Click <button>Submit</button> to upload the data to the UCSC Genome Browser. You will be taken
   to a new page where you can view all your uploaded custom tracks. Here, you can edit the
   annotation data, or remove any custom tracks.
 
   There is also a drop-down menu to view the data in other tools, such as:
 
   - Genome Browser
   - Table Browser
   - Data Integrator
   - Variant Annotation Integrator
 
   Clicking on the chromosome hyperlink, e.g. chr21, in the table will take you to the Genome
   Browser image to view the data.
 
   </div>
   <div class="col-md-6">
   ```image
   src=/images/tutorialImages/gif/hgCustomStep5.gif
   width=90%
   ```
   </div>
 </div>
 
 ## Additional Help
 
 - [Custom Track User Guide](/goldenPath/help/customTrack.html)
 - [Contact UCSC](/contacts.html)